Objectives: We sought to evaluate the effects of omega-3 and vitamin E co-supplementation on carotid intima-media thickness (CIMT) and inflammatory factors in patients with polycystic ovary syndrome (PCOS). Methods: This randomized, double-blind, placebo-controlled trial was done among 60 women with PCOS. Participants were randomly assigned into two groups (n = 30 each group) and assigned to take either 1000 mg omega-3 plus 400 IU vitamin E supplements or a placebo for 12 weeks. Results: Compared with placebo, omega-3 and vitamin E co-supplementation led to significant decreases in maximum levels of left CIMT (-0.006±0.006 vs. +0.002±0.007 mm, p < 0.001), mean levels of left CIMT (-0.005±0.006 vs. +0.002±0.010 mm, p = 0.010), maximum levels of right CIMT (-0.006±0.010 vs. +0.006±0.010 mm, p = 0.010), and mean levels of right CIMT (-0.005±0.005 vs. +0.001±0.010 mm, p = 0.020). Change in high-sensitivity C-reactive protein (hs-CRP) (-390.6±942.9 vs. +237.0±754.3 ng/mL, p = 0.006) was significantly different between the supplemented patients and placebo group. We did not observe any significant effect in plasma nitric oxide (NO) values following supplementation with omega-3 plus vitamin E compared with the placebo. Conclusions: Co-supplementation with omega-3 and vitamin E for 12 weeks among patients with PCOS had beneficial effects on CIMT and serum hs-CRP values, but unchanged NO values.